Gene Designer- a brilliant software tools that allows one to combine building blocks such as regulatory DNA elements (promoters, ribosome-binding sites) with amino acid sequences, affinity & protease cleave tags and cloning features and codon optimize for any expression host.

CLC Free Workbench - allows basic sequence analysis such as open reading frame determination, restriction site analysis, translation from DNA/ RNA to proteins, alignments, and tree reconstruction in a single window format.

Genome2D - is for the visualization of transcriptome and other customized data sets (visualizes a bacterial genome with all relevant information such as gene orientation, operon structure, transcriptional terminators or regulator binding sites) on linear chromosome maps constructed from annotated bacterial genome sequences. For a complete list of what this incredible program will do see here. Images and data tables from Genome2D can easily be exported for further use in other presentation programs. (Reference: Baerends, R.J.S.,et al. (2004) Genome Biology, 5:R37).

EMBOSS (European Molecular Biology Open Source Software Suite) can be downloaded from here.

MB DNA Analysis (Oleg Simakov) - MB is a free multi-functional DNA/protein analysis program. It's main advantage is that it combines all of the most widely used features needed for an advanced molecular analysis of genomic/proteomic data. Features of MB include a fast restriction analysis algorithm (included plasmid / linear DNA drawing), promoter analysis, calculation of molecular weights and chemical properties of proteins, prediction of the secondary protein structures (after Chou-Fasman). Protein analysis also includes sequence translation and codon usage table calculation. Other features: hierarchical multiple sequence alignment tool (with a feature to compare secondary structure of proteins), phylogenetic tree building, dot plot, estimation of isoelectric point for proteins, primer design. A tool for the structural analysis of alpha helices is also included in the main package. GenePalette allows genome sequence visualization and navigation. Users can download from NCBI’s GenBank database large or small segments of genome sequence from a variety of organisms preserving the gene annotation that is associated with that sequence. Sequence elements of interest (transcription factor binding sites, etc. can be searched for and identified in the loaded sequence, and then clearly visualized within a colorful graphical representation of gene organization.

UniPro DPview (UniPro Bioinformatics Group, Russia) - this is a tool for finding and analyzing matches between genomes. The user can examine the matches, selecting them directly on the dotplot matrix. This program also allows one to build local alignments with specified parameters (match cost, mismatch and gap penalties), using a modification of the classic Smith-Waterman algorithm. It is possible to find not only the best alignment score-wise, but also so-called "suboptimal" ones which have slightly lesser scores.

SEQtools is a program package for routine handling and analysis of DNA and protein sequences. The package includes general facilities for sequence and contig editing, restriction enzyme mapping, translation, and repeat identification.

ZCURVE - is a new highly accurate system for recognizing protein coding genes in bacterial and archaeal genomes based on the Z curve theory of DNA sequence (Reference: F.-B. Guo, H.-Y. Ou & C.-T. Zhang (2003). Nucleic Acids Res. 31: 1780-1789). I have experience some problems in downloading their E. coli genome sequence for analysis and have attached a new version.

DNA for Windows is a compact, easy to use DNA analysis program, ideal for small-scale sequencing projects.

loopDloop is a tool for drawing RNA secondary structures in molecular biology.

Chromas will display and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF, Li-Cor and Visible Genetics OpenGene sequencers can create. N.B. only the older versions of the software are free.

FinchTV - Another useful tool for viewing and editing electropherograms.

G-language Genome Analysis Environment provides a greater variety of useful genome analysis tools compared to most existing analysis software packages, and is also easily pluggable. All of its tools are accessible as Perl modules. To get started download genome files from GenBank in *.gbk format (GenBank flat file format).

WinGene - Used to give the reverse complement a given sequence, translate the sequence in all reading frames and identify ORFs (Export polypeptides encoded by a given ORF into WinPep), perform a oligomer analysis (base composition and melting temperature), and perform a restriction analysis. GeneDoc is a full featured multiple sequence alignment editor, analyzer and shading utility for Windows.

GeSTer (V. Nagaraja, Indian Institute of Science, Bangalore. India) - is extremely useful in locating stem-loop structures, including rho-independent terminators in annotated genomes. Since it does not run conveniently on Windows XP see how you can modify the *.gbk file so that it works.

RepeatAround - is designed to find “direct repeats”, “inverted repeats”, “mirror repeats” and “complementary repeats”, from 3 bp to 64 bp length, in circular genomes. It processes input files directly extracted from GenBank database and several genomes can be input simultaneously. The program provides visualisation of the repeats location in the genomic structure and the search for specific motifs is also possible. Outputs can be obtained in a spreadsheet containing information on the number and location of the repeats. The software also generates random circular genomes, for statistical evaluations or comparisons between observed and expected repeats distributions.(Reference: A. Goios et al. 2006. Mitochondrion. 6: 218-224.)

Staden Package - consists of a series of tools for DNA sequence preparation (pregap4), assembly (gap4), editing (gap4) and DNA/protein sequence analysis (spin). The package was originally developed at the MRC-LMB in Cambridge. It is now open source (BSD licence) and is hosted on sourceforge.net.

Seqool - sequence analysis software designed primarily for searching biological signals in nucleic acid sequences. The sequence analysis program package provides several pattern recognition models, but it also includes the most common sequence analysis statistics, such as GC content, codon usage, etc.

RepeatAround - is designed to find “direct repeats”, “inverted repeats”, “mirror repeats” and “complementary repeats”, from 3 bp to 64 bp length, in circular genomes. It processes input files directly extracted from GenBank database or simple sequence. Outputs can be obtained in a spreadsheet containing information on the number and location of the repeats. (Reference: Goios A et al. 2006. Mitochondrion 6: 218-224.)

ApE Plasmid Editor (M. Wayne Davis, Univ. Utah, U.S.A.)highlights and draws graphic maps using feature annotations from GenBank and EMBL files; creates graphic restriction maps - linear or circular with features indicated and allows BLAST analyses along with a number of other useful features.

pDRAW32 DNA analysis software by AcaClone software (Kjeld Olesen). pDRAW lets you enter a DNA name and coordinates for genetic elements, such as genes, to be plotted on your DNA plots.

Plasmid Processor (Department of Biochemistry and Biotechnology, University of Kuopio, Finland) - is a simple tool for plasmid presentation for scientific and educational purposes. It features both circular and linear DNA, user defined restriction sites, genes and multiple cloning site. In addition you can manipulate plasmid by inserting and deleting fragments. Created drawings can be copied to clipboard or saved to disk for later use. Printing from within the program is also supported.

BVTech Plasmid - with this program you can draw circular or linear plasmid map with double strands or single strand. You can label the plasmid with genes and restriction sites in different colors, text, and styles.

PlasmaDNA (PLAsmid MAnipulation) - is a DNA analysis and manipulation program which is simple to learn and to use, and contains multiple features designed to help with the design of a successful cloning strategy, the generation of the sequences of new clones, and, the archiving of the cloning strategy. (Reference: A. Angers-Loustau et al. 2007. BMC Mol. Biol. 8:77

Picky is an oligo microarray design program that identifies probes that are very unique and specific to input sequences. These calculations are based on parameters inputted by the user including optimal probe length, ideal percentage of guanine and cytosine content, target-melting temperature, salt concentration and the maximum length to which a target sequence matches any non-target sequence. (Reference: H.-H. Chou et al. (2004) Bioinformatics 20: 2893-2902).Download genome *.ffn files from GenBank for use with this program. N.B. Unfortunately these files do not include the gene names only their coordinates.

GenomePrimer is a program that provides a high-throughput method to select, with minimal user intervention and maximum flexibility, the most unique regions within DNA sequences and design primers that meet certain preset criteria. (Reference:S.A.F.T. van Hijum et al. (2003) Bioinformatics 19: 1580-1582).

AutoDimer - AutoDimer was packaged for installation using Visual Basic 6.0 and was developed to rapidly screen previously selected PCR primers for primer-dimer and hairpin interactions. It was originally created to assist in the development of multiplex PCR assays for probing STR and SNP markers for forensic purposes.

AiO (All in One) is a program for Windows, that combines typical DNA/protein features such as plasmid map drawing, finding of ORFs, translate, backtranslate, primer design and virtual cloning. AiO uses databases that allow the management of oligonucleotides, oligonucleotide-manufacturers, restriction enzymes, structural DNA and program users in a multi-user/multi-group environment. (Reference: Karreman C. (2002) Bioinformatics. 18:884-885).

Fast PCR - is based on the new approach in design PCR primers, alignment and repeat sequence searching. Program can work with several sequences simultaneously and the size of files up to 2Gb, multiplex PCR primers design and "in silico" PCR is supported. The program is convenient for search homology in a personal database is similar to BLAST and also others bioinformatics tools are included. Powerful and fast search of all types of repeats in DNA based on the new theory of search of repeats is developed. Now the program supports clustering sequences (R. Kalendar & A.H. Schulman, Institute of Biotechnology, Univ. Helsinki, Finland).

- Oligo Analyzer is a simple tool to determine primer properties like Tm, GC%, primer loops, primer dimers and primer-primer compatibility. All you have to do is to paste or type primer sequence and let Oligo Analyzer to calculate all important primer properties mentioned above. Readme

- Oligo Explorer is a tool to search primers and primer pairs. The program analyzes all important primer properties like Tm, GC%, primer loops, primer dimers and etc. Readme

ANTHEPROT (ANalyse THE PROTeins) is the result of biocomputing activity at the Institute of Biology and Chemistry of Proteins (Lyon, France)

STORM - this program extracts protein sequences after ORF prediction and subsequently performs an automatic analysis for each of the proteins. This analysis consists of web-based similarity searches (BLASTp and FASTA) as well as Pfam predictions and Protparam calculations of protein physicochemical properties. The raw output for these analyses is then analysed and summarized. (Reference: Lavigne, R. et al. (2003.) Applied Bioinformatics 2: 177-179).

BioEditor(Peng Yang, Paul A. Craig, Philip E. Bourne, & David Goodsell, San Diego Supercomputer Center, U.S.A.) - is a tool to bridge the gap between the printed literature and current Internet presentation formats. This application that can be used to prepare and present structure annotations containing formatted text, graphics, sequence data, and interactive molecular views. It require that MDL Chime be installed.

Yasara (Gregor H?genauer, Günther Koraimann, & Andreas Kungl [Univ. Graz, Austria]; & Gert Vriend [Univ. Nijmegen, the Netherlands]) is an awesome program for viewing an labeling 3-D structures. To visual your own pdb structure right click and chose open with (Yasara). This free program is part of a more extensive molecular modeling package.

NOC (Chenmengen & Cang, Institute of Biophysics, Chinese Academy of Sciences [IBP-CAS]) is a program to model/build, visualize and analysis protein structure and includes: easy addition/delete of water and heteroatoms, comparison of similar structures, predict possible motifs (sites) in the molecule, high quality rendering and many types of output (such as TIFF, PNG, BMP), and WYSIWYG labeling method.

RasMol is software for looking at molecular structures. It is very fast: rotating a protein or DNA molecule shows its 3D structure.

Deep View (Swiss-PdbViewer) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface

Scion Image may be used to capture, display, analyze, enhance, measure, annotate, and output images.

MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.

- Biodesigner is a molecular modeling and visualization program for personal computers which is capable of creating homologous models of proteins, evaluate, and refine the models.

RasTop - RasTop is a molecular visualization software adapted from the program RasMol by wrapping a user-friendly graphical interface around the "RasMol molecular engine". The software allows several molecules to be opened in the same window and several windows to be opened at the same time. Through an extended menu and a command panel, users can manipulate numerous molecules rapidly and learn about them. Work sessions are saved in script format and are fully regenerated with a simple mouse click.

ClustalX is a windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results. Online help can be found here. (Reference: J.D. Thompson et al. (1997). Nucleic Acids Research 24: 4876-4882).

BioEdit is a mouse-driven, easy-to-use sequence alignment editor and sequence analysis program designed and written by Tom Hall (North Carolina State University). It also provides BLAST capability on local databases.

LalnView is a graphical program for visualizing local alignments between two sequences (protein or nucleic acids). Sequences are represented by colored rectangles to give an overall picture of the similarities between the two sequences. Blocks of similarity between the two sequences are colored according to the degree of identity between segments.

CHROMA takes your aligned multiple sequence data, annotates residues according to a consensus and displays the alignment using different font formats (text and background colours, bold and italic). The formatted annotation can be sent directly into Microsoft Word, or saved to a file or Windows Clipboard in both HTML and "Rich Text" Formats. (Reference: L. Goodstadt & C.P. Ponting. (2001) Bioinformatics 17: 845-846).SeaView is a graphical multiple sequence alignment editor developed by Manolo Gouy. SeaView is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows ones to manually edit the alignment, and also to run DOT-PLOT or CLUSTAL programs to locally improve the alignment.

HyPhy - intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. HYPHY was designed with maximum flexibility in mind and to that end it incorporates a simple high level programming language which enables the user to tailor the analyses precisely to his or her needs. These include relative rate and ratio tests, several methods of ML based phylogeny reconstruction, bootstrapping, model selection, positive selection, molecular clock tests and many more (Reference: S.L. Kosakovsky et al.(2005) Bioinformatics 21:676-679).

TREECON - is a software package developed primarily for the construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences. It offers considerable opportunity to change the appearance of the tree. (Reference: Van de Peer, Y. & De Wachter, Y. (1994) Comput. Applic. Biosci. 10, 569-570).

TREEMAP is designed as a simple tool for visually comparing host and parasite phylogenies: you can view the host and parasite trees, interactively create reconstructions of the history of the host-parasite association, perform randomization tests of tree similarity, and (if you have branch length information such as might be obtained from DNA sequence data) compare branch lengths in the two trees.

Treefinder (Gangolf Jobb, Statistical Genetics and Bioinformatics, University of Munich) computes phylogenetic trees from nucleotide sequences. Using the widely accepted Maximum Likelihood method, it is offering a variety of evolutionary models up to the general time reversible model with Gamma and codon position rate heterogeneity among sites. The confidence of inferred relationships may be assessed by bootstrap analysis or, alternatively, by a local rearrangement paired-sites method (LRP). Linus and Mac versions also available.

PopG genetic simulation program (Joe Felsenstein, University of Washington) simulates evolution of a single locus in the presence of natural selection, mutation, migration, and genetic drift.

Tree-Puzzle (H.A. Schmidt, K. Strimmer, M. Vingron, & A. von Haeseler, Germany) constructs phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated under the clock- assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment.

Modeltest is a program that uses hierarchical likelihood ratio tests (hLRT) to compare the fit of the nested GTR (General Time Reversible) family of nucleotide substitution models. Additionally, it calculates the Akaike Information Criterion estimate associated with the likelihood scores. (Reference: Posada, D. & K. A. Crandall. 1998. Bioinformatics14: 817-818).

TreeView provides a simple way to view the contents of a NEXUS, PHYLIP, or other format tree file. This program can be coupled with an analysis package called FreeTree written by Dr. Jaroslav Flegr (Charles University, Prague, Czech Republic).

GeneTree is an experimental program for comparing gene and species trees.

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies. PHYLIP is the most widely-distributed phylogeny package, and competes with PAUP to be the one responsible for the largest number of published trees (Joe Felsenstein, University of Washington, U.S.A.).

MrBayes is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods. MrBayes has a console interface and uses a modified NEXUS format for data and batch files. It handles a wide range of probabilistic models for the evolution of nucleotide and amino acid sequences, restriction sites, and standard binary data. The user can set the priors used for the parameters and search for trees under topological constraints.

Processor of Sequences (ProSeq) is a Windows 95 / NT program for convenient sequence alignment editing and various population-genetic analyses. PROSEQ was written by Dmitry Filatov.

PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. TipDate - a program to estimate the rate of molecular evolution and time-scale of a phylogeny from dated sequences. Written by Andrew Rambaut. NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. Written by Manolo Gouy.

ISIS/Draw is a chemically intelligent drawing package that enables you to draw chemical structures using the same intuitive signs and symbols used for paper sketches. You can insert your ISIS/Draw sketches into documents, Web pages, spreadsheets, and presentations. You can also use ISIS/Draw to create structures to register into 2D and 3D molecule, polymer, and reaction databases, and to create queries for searching these databases.

Xenu's Link Sleuth (TM) is a spidering software that checks Web sites for broken links. Link verification is done on "normal" links, images, frames, plug-ins, backgrounds, local image maps, style sheets, scripts and java applets. It displays a continously updated list of URLs which you can sort by different criteria. I use this program to verify if the links on Online Analysis Tools are working.

Paint.NET is a photo and image editing tool designed for computers running Microsoft Windows XP or Windows 2000. It serves the digital imaging community as a free alternative to the standard paint application included with Windows. It brings powerful features to the desktop, a myriad of special effects, plug-in extensibility, and layer manipulation. It enhances the image editing experience for tablet owners with Windows XP Tablet Ink support. Digital photographers and artists can enhance their images with features and effects such as levels adjustment, cross-layer cloning, anti-aliased tools, motion blur, and red eye removal.

TinyQuant is a graphical display program designed for analysis and limited manipulation of images obtained by scanning of gels or autoradiographs. Useful for integrating densities of gel bands in 16 bit greyscale (PC or Mac format ".gel" or TIFF files) or 24 bit RGB TIFF images, and for converting these to 8 bit greyscale TIFFs.

A Smaller GIF - Pedagoguery Software Inc. provides a variety of free software packages for both Macintosh and Windows computers. This program reduces the size of animated GIFs without affecting their appearance in any way.

GIMP is the GNU Image Manipulation Program. It is a freely distributed piece of software for such tasks as photo retouching, image composition and image authoring. It works on many operating systems, in many languages. The GIMP animation package, is also now available